BOLD fMRI in rodents has been used to investigate brain functions in normal and diseased conditions. Until now, most animal fMRI have used anesthetics to reduce animal stress and minimize motions. Because anesthesia affects neurovascular coupling, maintaining the proper physiological condition under anesthesia is important. However, it is challenging in mice due to the limitation of physiological monitoring and high sensitivity to anesthetics used. Here we introduced ketamine and xylazine anesthesia in mice. Then, to examine the variability of fMRI response and indirectly measure the physiological condition, we use the resting state fMRI (RS-fMRI), which detects intrinsic brain state and connectivity.